GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Streptococcus massiliensis 4401825

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_018372539.1 BN415_RS01710 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_000341525.1:WP_018372539.1
          Length = 511

 Score =  126 bits (316), Expect = 1e-33
 Identities = 74/229 (32%), Positives = 128/229 (55%), Gaps = 13/229 (5%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           ++E++ +TK FG   A   + L L  GE+  L+G NGAGK+TL N+L G+ EP+ G + +
Sbjct: 6   VIEMRDITKIFGEFVANDKINLHLRRGEIHALLGENGAGKSTLMNMLAGLLEPTSGEIVV 65

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
           +G  +   SP K A+LG+G   Q+  L +  TV +N+++  G+   +H            
Sbjct: 66  NGKTVQLDSPSKAAALGIGMVHQHFMLVEAFTVAENIIL--GSETTKHGVLD------IK 117

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
           K+ +E+K    EL + + L  D     +++S G Q+R+EI++ L     IL  DEP A +
Sbjct: 118 KATQEIK----ELSEKYGLAVDPSAKVEDISVGAQQRVEILKTLYRGADILIFDEPTAVL 173

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLI 231
            P E  EL ++++ +  E K +++LI H ++ +  V +R+ V+  G+ I
Sbjct: 174 TPSEIEELEKIMKNLVKEGK-SLILITHKLDEIRAVADRVTVIRRGKSI 221



 Score = 84.0 bits (206), Expect = 6e-21
 Identities = 62/255 (24%), Positives = 135/255 (52%), Gaps = 16/255 (6%)

Query: 3   LLEVKQLTKHFG-GLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61
           +L +K L  +   G+ AV  ++L++  GE+VG+ G +G G++ L   +TG+ +  EGT+T
Sbjct: 258 ILSIKDLVVNENRGIPAVKGLSLDVRAGEIVGIAGIDGNGQSELVQAITGLRKVKEGTIT 317

Query: 62  LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVL---IAFGNHHKQHVFTSFLRL 118
           + G  + G SP KI  + +    ++    +D  VLD ++   IA   ++K+ +  + +  
Sbjct: 318 IKGENVVGHSPRKITEMQVSHVPED--RHRDGLVLDMMISENIALQTYYKEPLSKNGI-- 373

Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETL-AKNLSYGQQRRLEIVRALATEPKILFLDE 177
                +   + + A +L+K FD+   +E + A  LS G Q++  + R +   P +L + +
Sbjct: 374 ----LNYNNITSYAKKLMKEFDVRAASEFVPASALSGGNQQKAIVAREIDRNPDLLIVSQ 429

Query: 178 PAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPD 237
           P  G++      + + +   +D+ K  ++++  +++ ++ +++RI V+  G++     P+
Sbjct: 430 PTRGLDVGAIEYIHKRLIEERDKGK-AVLVVSFELDEILNLSDRIAVIHDGKIQGIVLPE 488

Query: 238 EIKTNKRVIEAYLGG 252
           E  TNK+ +   + G
Sbjct: 489 E--TNKQELGILMAG 501


Lambda     K      H
   0.319    0.139    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 322
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 254
Length of database: 511
Length adjustment: 29
Effective length of query: 225
Effective length of database: 482
Effective search space:   108450
Effective search space used:   108450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory